GH1 p.Arg160=
c.480G>T · VCV3718730
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00797%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.49 | GERP -3.4 |
| Overall | ||
| CADD | 0.775 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00797%
European (non-Finnish) · 94/1,179,860 alleles
Filtering AF
0.00664%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00616%
Overall
0.0062%
100/1,613,842 alleles · very rare
exomes 99/1,461,670 · genomes 1/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00797% | 12,552 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,234 |
| African / African-American | 0.00267% | 37,453 |
| Admixed American | 0.00167% | 60,002 |
| Finnishnot grpmax-eligible | 0.00156% | 64,042 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- GH1
- Protein
- p.Arg160=
- Coding
- c.480G>T
- MANE Select
- NM_000515
- Type
- single nucleotide variant
- Location
- chr17:63917483 (GRCh38)
- Gene constraint
- LOEUF 0.838 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 10 PDB
Similar variants
- GH1 c.291+1G>A Pathogenic ★★ same type
- GH1 c.291+5G>A Pathogenic ★★ same type
- GH1 p.Arg209His Pathogenic ★★ ⚠ same type
- GH1 p.Glu82Asp Uncertain significance ★★ ⚠ same type
- GH1 c.456+19G>T Benign/Likely benign ★★ same type
- GH1 c.-38A>C Benign/Likely benign ★★ same type
- GH1 c.-4T>G Benign/Likely benign ★★ same type
- GH1 p.Phe51Tyr Benign/Likely benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/gh1-p-arg160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown